LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -64.175504 0.0000000) to (37.049647 64.175504 6.2925696) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6999457 5.7590140 6.2925696 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.175504 0.0000000) to (37.049647 64.175504 6.2925696) create_atoms CPU = 0.003 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6999457 5.7590140 6.2925696 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.175504 0.0000000) to (37.049647 64.175504 6.2925696) create_atoms CPU = 0.003 seconds 1249 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 34 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2472 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_036303866285_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10470.085 0 -10470.085 3782.0733 74 0 -10532.673 0 -10532.673 -9245.8519 Loop time of 2.19942 on 1 procs for 74 steps with 2472 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10470.0852863253 -10532.6633207841 -10532.6728706922 Force two-norm initial, final = 67.893292 0.36304011 Force max component initial, final = 13.201422 0.039133341 Final line search alpha, max atom move = 1.0000000 0.039133341 Iterations, force evaluations = 74 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1456 | 2.1456 | 2.1456 | 0.0 | 97.55 Neigh | 0.023963 | 0.023963 | 0.023963 | 0.0 | 1.09 Comm | 0.015687 | 0.015687 | 0.015687 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01418 | | | 0.64 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11821.0 ave 11821 max 11821 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 404554.0 ave 404554 max 404554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404554 Ave neighs/atom = 163.65453 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.148 | 6.148 | 6.148 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -10532.673 0 -10532.673 -9245.8519 29923.431 77 0 -10532.8 0 -10532.8 -5271.3623 29843.229 Loop time of 0.0942077 on 1 procs for 3 steps with 2472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10532.6728706922 -10532.800363687 -10532.8003702888 Force two-norm initial, final = 132.84638 0.54519695 Force max component initial, final = 105.88816 0.32239146 Final line search alpha, max atom move = 0.0032314194 0.0010417820 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091338 | 0.091338 | 0.091338 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005203 | 0.0005203 | 0.0005203 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00235 | | | 2.49 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11865.0 ave 11865 max 11865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 370066.0 ave 370066 max 370066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370066 Ave neighs/atom = 149.70307 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.285 | 6.285 | 6.285 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10532.8 0 -10532.8 -5271.3623 Loop time of 1.912e-06 on 1 procs for 0 steps with 2472 atoms 156.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.912e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11865.0 ave 11865 max 11865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 388028.0 ave 388028 max 388028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388028 Ave neighs/atom = 156.96926 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.285 | 6.285 | 6.285 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -10532.8 -10532.8 37.007419 128.35101 6.2828651 -5271.3623 -5271.3623 -10.6332 -15820.735 17.281354 2.3714025 1036.1544 Loop time of 2.138e-06 on 1 procs for 0 steps with 2472 atoms 187.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.138e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11865.0 ave 11865 max 11865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194014.0 ave 194014 max 194014 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 388028.0 ave 388028 max 388028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388028 Ave neighs/atom = 156.96926 Neighbor list builds = 0 Dangerous builds = 0 2472 -10532.8003702888 eV 2.37140252631395 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02